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- PDB-9rw4: Egalitarian-BicD in complex with hSL1 of the hairy localization e... -

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Basic information

Entry
Database: PDB / ID: 9rw4
TitleEgalitarian-BicD in complex with hSL1 of the hairy localization element (Structure B)
Components
  • Egalitarian, isoform B
  • Protein bicaudal D
  • hSL1
KeywordsRNA BINDING PROTEIN / Complex / Transport / Localization
Function / homology
Function and homology information


larval salivary gland morphogenesis / oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / intracellular mRNA localization involved in pattern specification process / microtubule anchoring at microtubule organizing center / germarium-derived egg chamber formation / bicoid mRNA localization / regulation of oskar mRNA translation / oocyte microtubule cytoskeleton polarization / oocyte microtubule cytoskeleton organization / germarium-derived oocyte fate determination ...larval salivary gland morphogenesis / oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / intracellular mRNA localization involved in pattern specification process / microtubule anchoring at microtubule organizing center / germarium-derived egg chamber formation / bicoid mRNA localization / regulation of oskar mRNA translation / oocyte microtubule cytoskeleton polarization / oocyte microtubule cytoskeleton organization / germarium-derived oocyte fate determination / pole plasm oskar mRNA localization / positive regulation of synaptic vesicle exocytosis / protein transport along microtubule / cargo adaptor activity / COPI-independent Golgi-to-ER retrograde traffic / positive regulation of clathrin-dependent endocytosis / chaeta development / transport along microtubule / RNA transport / oocyte axis specification / clathrin heavy chain binding / cytoskeletal anchor activity / intracellular mRNA localization / nucleobase-containing compound metabolic process / oogenesis / regulation of endocytosis / dynein complex binding / dynactin binding / mRNA transport / synaptic vesicle endocytosis / 3'-5' exonuclease activity / regulation of microtubule cytoskeleton organization / small GTPase binding / presynapse / cytoskeleton / mRNA binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Egalitarian winged helix domain / Bicaudal-D protein / Microtubule-associated protein Bicaudal-D / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein bicaudal D / Egalitarian, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSingh, K. / Chilaeva, S. / McClintock, M.A. / Bullock, S.L. / Carter, A.P.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 197-2021European Union
CitationJournal: To Be Published
Title: Structures of Egl-BicD reveal how diverse mRNAs are selected for subcellular localization
Authors: Singh, K. / Chilaeva, S. / McClintock, M.A. / Bullock, S.L. / Carter, A.P.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein bicaudal D
B: Protein bicaudal D
D: Egalitarian, isoform B
C: Egalitarian, isoform B
E: hSL1
F: hSL1


Theoretical massNumber of molelcules
Total (without water)446,8266
Polymers446,8266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein bicaudal D


Mass: 89073.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: BicD, CG6605 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16568
#2: Protein Egalitarian, isoform B / Egalitarian / isoform C


Mass: 113198.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: egl, Dmel\CG4051, egal, EGL, Egl, CG4051, Dmel_CG4051 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9W1K4
#3: RNA chain hSL1


Mass: 21141.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Egalitarian-BicD in complex with hSL1 of the hairy localization element
Type: COMPLEX
Details: Egalitarian-BicD in complex with the stem loop 1 (hSL1) of the Drosophila hairy mRNA localization element
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 7.3
Details: 25 mM HEPES pH 7.3, 150 mM KCl, 1 mM MgCl2, 1mM DTT, 0.00125% IGEPAL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraXmodel fitting
9PHENIX1.20_4459model refinement
10cryoSPARC4initial Euler assignment
11RELION5final Euler assignment
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42550 / Symmetry type: POINT
Atomic model buildingDetails: Predicted models used for all components / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028446
ELECTRON MICROSCOPYf_angle_d0.54711906
ELECTRON MICROSCOPYf_dihedral_angle_d12.7932076
ELECTRON MICROSCOPYf_chiral_restr0.0351498
ELECTRON MICROSCOPYf_plane_restr0.0031296

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